Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site.

ABSTRACT: Mechanisms for transcription factor recognition of specific DNA base sequences are well characterized and recent studies demonstrate that the shape of these cognate binding sites is also important. Here, we uncover a new mechanism where the transcription factor GabR simultaneously recognizes two cognate binding sites and the shape of a 29 bp DNA sequence that bridges these sites. Small-angle X-ray scattering and multi-angle laser light scattering are consistent with a model where the DNA undergoes a conformational change to bend around GabR during binding. In silico predictions suggest that the bridging DNA sequence is likely to be bendable in one direction and kinetic analysis of mutant DNA sequences with biolayer interferometry, allowed the independent quantification of the relative cont

SUBMITTER: Al-Zyoud WA 

PROVIDER: S-EPMC4756830 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature